X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FResidue.java;h=edef5f1bcfe22cb7826fed42dce87bbbc873a5e8;hb=refs%2Fheads%2Ffeature%2FJAL-3180colourAnnotationMenu;hp=6e95c8990578312fd99245c0a40b773a388811e1;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java
index 6e95c89..edef5f1 100755
--- a/src/MCview/Residue.java
+++ b/src/MCview/Residue.java
@@ -1,52 +1,57 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
-import java.util.*;
+import java.util.Vector;
public class Residue
{
- Vector atoms = new Vector();
+ Vector atoms;
int number;
int count;
- int seqnumber;
-
- public Residue(Vector atoms, int number, int count)
+ public Residue(Vector resAtoms, int number, int count)
{
- this.atoms = atoms;
+ this.atoms = resAtoms;
this.number = number;
this.count = count;
}
public Atom findAtom(String name)
{
- for (int i = 0; i < atoms.size(); i++)
+ for (Atom atom : atoms)
{
- if (((Atom) atoms.elementAt(i)).name.equals(name))
+ if (atom.name.equals(name))
{
- return (Atom) atoms.elementAt(i);
+ return atom;
}
}
return null;
}
+
+ public Vector getAtoms()
+ {
+ return this.atoms;
+ }
}